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    Josh Moore
    @joshmoore
    De nada.
    Curtis Rueden
    @ctrueden
    I am nearly done retiring the LOCI Trac instances. The public LOCI Software Trac is now archived here: https://uw-loci.github.io/tickets/
    I should have redirects from dev.loci.wisc.edu/trac/software/... to the right places very soon.
    I mention it here because nearly all of the tickets are Bio-Formats-related.
    Josh Moore
    @joshmoore
    :+1: thanks, Curtis. Probably will need to do the same for our instance soon.
    Curtis Rueden
    @ctrueden
    Let me know when you do; there are a lot of http://trac.openmicroscopy.org.uk/ome/intertrac links I'll need to fix then.
    (Unless you plan to keep those working.)
    Josh Moore
    @joshmoore
    Hmmm.... interesting. I'll have to check. Do you have a pointer to one?
    Curtis Rueden
    @ctrueden
    If you git clone git://github.com/uw-loci/tickets and then git grep trac.openmicroscopy you'll see 119 examples. :wink:
    There are some in https://github.com/imagej/tickets, the other Trac instance, as well.
    Josh Moore
    @joshmoore
    One of those links looks to already be broken :( We'll try to fix via a redirect.
    Cool, thanks.
    Curtis Rueden
    @ctrueden
    FYI, netcdf-java v5.0.0 was recently released: https://github.com/Unidata/netcdf-java/releases/tag/v5.0.0
    Josh Moore
    @joshmoore
    thanks. I passed the info along.
    NicoKiaru
    @NicoKiaru

    I'm sttrugling a bit with something that looked simple... Maybe you can help me ? Basically I want to use the [https://github.com/ome/bioformats/blob/develop/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java] (ImageConverter) class within a Fiji plugin. Which dependency should I declare within my pom file ? I tried:

            <dependency>
                <groupId>ome</groupId>
                <artifactId>pom-bio-formats</artifactId>
                <version>6.2.0</version>
            </dependency>

    Which is in the Scijava Maven repository, but apparently IntelliJ do not find the ImageConverterclass. I'm a bit out of options right now...

    Josh Moore
    @joshmoore
    To do the same, I use bio-formats-tools. See https://github.com/spacetx/spacetx-writer/blob/master/build.gradle#L32, but note that that's a duplicate. The version from the ome/bioformats repository has not yet been removed.
    NicoKiaru
    @NicoKiaru
    Yeepee! Thanks @joshmoore . I do not really understand the logic behind, but at least I can work with that.
    Josh Moore
    @joshmoore
    :+1: If you run into any problems, perhaps open issues against https://github.com/ome/bio-formats-tools/issues -- I know of a few off the bat, like the constructor is private.
    (issues or PRs of course ;) )
    NicoKiaru
    @NicoKiaru
    Oki doki, I'll try the to use the main method first, which is public. I'll let you know how that goes ;-)
    Josh Moore
    @joshmoore
    (That's what I did as well.) Good luck.
    NicoKiaru
    @NicoKiaru
    Aaah, just found out there's no pyramid option in this package. Is there a way to have a version with it ? It seems pyramid options are only in the develop branch...
    Ah sorry there is... I have probably another problem is my function call. I'll dig
    Curtis Rueden
    @ctrueden
    We need a shovel award, for people like @NicoKiaru. Every time you dig and report back your findings, you earn points. These go on your CV and employers take it more seriously than journal impact factor. </daydream>
    NicoKiaru
    @NicoKiaru
    Ahahah I need a shovel to hide right now. Just found out I forgot to remove a space in the ' -pyramid-scale' argument. I had to go full debug to find out this string is not equal to '-pyramid-scale'.
    Curtis Rueden
    @ctrueden
    At least it only took a few minutes to solve!
    Josh Moore
    @joshmoore
    Cheers.
    Curtis Rueden
    @ctrueden
    FYI, netCDF Java developers are looking for feedback on their new public API.
    Josh Moore
    @joshmoore
    Thanks, @ctrueden. :thumbsup:
    NicoKiaru
    @NicoKiaru
    Hi! Is there a way to check in advance whether making a new memo file will be needed or not ? This could be a useful information to give to users. HCS dataset can take a few minutes to open when a memo file has to be re-created.
    Josh Moore
    @joshmoore
    Hey @NicoKiaru. I don't think so. Just asking the others now.
    The update notes say as much, but that's not overly useful.
    I'm pretty sure it's a runtime issue down inside of Kryo
    Melissa adds that there's a skipSave method which you could set, so when kryo throws an exception loadMemo will return null. On the next opening, then you'd want/need to save.
    NicoKiaru
    @NicoKiaru
    :+1: sounds good! I'll try it
    Josh Moore
    @joshmoore
    :thumbsup:
    odinsbane
    @odinsbane
    I was looking at the ND2 reader https://github.com/ome/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/NativeND2Reader.java and it says that JAI is required. Is that bundled with the bioformats_package.jar? It seemed to work, but it takes a really long time to open files.
    Nevermind, I opened the jar file and found it.
    odinsbane
    @odinsbane
    We have some 1-5TB data files in nd2 format, and I would like to convert them to something the bigdataviewer can manage. I suppose an h5 file with associated xml.
    Niko Ehrenfeuchter
    @ehrenfeu
    @odinsbane I might be wrong (my memory is not the best about it), but I believe you need to open the .nd2 right away with BDV - it will use Bio-Formats under the hood and create the appropriate .h5 file for you.
    But others here will know better for sure...
    odinsbane
    @odinsbane
    Ill give it a shot.